Params: release/cmzasha --no-stderr --filter 110 25 /home/kasiaw/Rfam_7.0/CM/RF00238.cm /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta 1 specfile /home/kasiaw/results/Tetrahymena_thermophila.fasta/RF00238_ctRNA_pND324/RF00238_at25.filterspec Build: release Host: node001 pid: 12439 ---time: Mon Jul 4 15:06:36 2005 ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----specfile: hmm /home/kasiaw/Rfam_7.0_filters/RF00238_Saureus_compact.hmm hmm /home/kasiaw/Rfam_7.0_filters/RF00238_Saureus_expanded.hmm ----hmm-from-cmFileName: /home/kasiaw/Rfam_7.0/CM/RF00238.cm ----hmm-build-info: ;(default construction of HMM) Params: release/cmzasha --create-rigorous-filter 110 25 /home/kasiaw/Rfam_7.0/CM/RF00238.cm /home/kasiaw/Rfam_7.0_filters data/default.filtercreationspec Build: release Host: cs007 pid: 20892 ;Params: release/cmzasha --create-rigorous-filter 110 25 /home/kasiaw/Rfam_7.0/CM/RF00238.cm /home/kasiaw/Rfam_7.0_filters data/default.filtercreationspec Build: release Host: cs007 pid: 20892 ----2struct-info: only-hmm ----hmm-from-cmFileName: /home/kasiaw/Rfam_7.0/CM/RF00238.cm ----hmm-build-info: ;(default construction of HMM) Params: release/cmzasha --create-rigorous-filter 110 25 /home/kasiaw/Rfam_7.0/CM/RF00238.cm /home/kasiaw/Rfam_7.0_filters data/default.filtercreationspec Build: release Host: cs007 pid: 20892 ;Params: release/cmzasha --create-rigorous-filter 110 25 /home/kasiaw/Rfam_7.0/CM/RF00238.cm /home/kasiaw/Rfam_7.0_filters data/default.filtercreationspec Build: release Host: cs007 pid: 20892 ----2struct-info: only-hmm ----cmFile: /home/kasiaw/Rfam_7.0/CM/RF00238.cm (global) ----CM-scanning-logic: Infernal-0.55 ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #14,emb|8254028| 344051 bp 2 contigs ----isReversed: 1 ----hitSequence: UGAUAAUUUAUUCCAUUAUGUAUAAUUUAAUUUUUUAUUAAUAAUCUAUUUGGUUAUCUUUUCAUAAUUUAUUUAUUAAAUCA ----ssRNAplot: ...(((.((((((......)))))))))....((((((((((((................))))))))))))........... ----hitGC: 0.120482 ----pairStats: 23,2,0,7 hit 0 : 17050 16968 (rev) 28.64 bits :::<<<<<<<<<<_.____>>>>>>>>>>----<<<<<<<<<<<<<______________ 1 UAgaAAgaugCuCC.UUGUGaGuguuUUuaaaUAaGCAUAGAGAAagUCaUUUuGcgGuG 59 U+ +AA+:::::CC UU UG::::: UU+AA+U: ::AU A: AA AUUU G +U 327002 UGAUAAUUUAUUCCaUUAUGUAUAA-UUUAAUUUUUUAU-UAAUAAUCUAUUUGGUUAUC 327059 ___>>>>>>>>>>>>>::::::::::: 60 aAuuUUCUCUAUGCuUUUAUUAUAUCA 86 +UUU :U AU:: :UUAUUA AUCA 327060 -UUUUCAUA-AUUUAUUUAUUAAAUCA 327084 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #354,emb|8254429| 128373 bp 1 contigs ----isReversed: 1 ----hitSequence: UAAUUAGAUUAGGUACAUUUUUUGAUAGUGUAAAUUUUAAAUAAAAAUAAAUAUUUUGGUUUGAUUGUUUUUAUUUAUUUAUUAUAAAA ----ssRNAplot: .....((((((((((......)))))))))).....(((((((((((((................)))))))))))))........... ----hitGC: 0.123596 ----pairStats: 23,0,2,5 hit 1 : 9467 9379 (rev) 25.48 bits :::..<<<<<<<<<<_.____>>>>>>>>>>-.---<<<<<<<<<<<<<___________ 1 UAg..aAAgaugCuCC.UUGUGaGuguuUUua.aaUAaGCAUAGAGAAagUCaUUUuGcg 56 UA A:A::: ::C UU U:: :::U:UA A+U: ::AUA:A:A A + AUUUUG 118907 UAAuuAGAUUAGGUACaUUUUUUGAUAGUGUAaAUUUUAAAUAAAAAUAAAUAUUUUGGU 118966 ______>>>>>>>>>>>>>::::::::::: 57 GuGaAuuUUCUCUAUGCuUUUAUUAUAUCA 86 UG AUU U:U:UAU:: :UUAUUAUA A 118967 UUG-AUUGUUUUUAUUUAUUUAUUAUAAAA 118995 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #478,emb|8254609| 555380 bp 1 contigs ----isReversed: 0 ----hitSequence: UGUAAAUAUGUAUUUGUACUUAUGUGUAUGUAUUAAUAUAUUAAUUUUUUUUGAAGAAAAUGUAAUAUAUAUUUAUUUUUUACCA ----ssRNAplot: ...((((((((((....))))))))))....(((((((((((((.................)))))))))))))........... ----hitGC: 0.141176 ----pairStats: 23,0,2,7 hit 2 : 397485 397569 (fwd) 25.05 bits :::<<<<<<<<<<_____>>>>>>>>>>----<<<<<<<<<<<<<_______________ 1 UAgaAAgaugCuCCUUGUGaGuguuUUuaaaUAaGCAUAGAGAAagUCaUUUuGcgGuGa 60 U++A A:A:G: UUGU :U:U:U UA UA ::AUA A: A: U +UUUUG++G A 397485 UGUAAAUAUGUAU-UUGUACUUAUGUGUAUGUAUUAAUAUAUUAAUUUUUUUUGAAGAAA 397543 __>>>>>>>>>>>>>::::::::::: 61 AuuUUCUCUAUGCuUUUAUUAUAUCA 86 AU:U :U UAU:: U U UU UA+CA 397544 AUGUAAUAUAUAUUUAUUUUUUACCA 397569 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #659,emb|8254645| 1076301 bp 3 contigs ----isReversed: 1 ----hitSequence: UAAAAAAUUUGUGCUUUAUUUAUUAUUUUUAGUAAUAAUUAAAAAAUUUUUAGCAAUAUUUUGAAUUAGUUUAUUAUAUUA ----ssRNAplot: ...((((((((((......))))))))))....(((((((((((...............)))))))))))........... ----hitGC: 0.0987654 ----pairStats: 23,2,1,6 hit 3 : 68736 68656 (rev) 31.24 bits :::<<<<<<<<<<_.____>>>>>>>>>>----<<<<<<<<<<<<<______________ 1 UAgaAAgaugCuCC.UUGUGaGuguuUUuaaaUAaGCAUAGAGAAagUCaUUUuGcgGuG 59 UA AAA:: : C UU U : ::UUU A UA ::AU :AAA + +UUU GC++U 1007566 UAAAAAAUUUGUGCuUUAUUUAUUAUUUUUAGUAAUAAUU--AAAAAAUUUUUAGCAAU- 1007622 ___>>>>>>>>>>>>>::::::::::: 60 aAuuUUCUCUAUGCuUUUAUUAUAUCA 86 AUUUU: AU:: UUUAUUAUAU A 1007623 -AUUUUG--AAUUAGUUUAUUAUAUUA 1007646 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #699,emb|8254659| 1557438 bp 6 contigs ----isReversed: 0 ----hitSequence: UAGAGAUUAAAUUCUGUUAGUGUUUUUAAUUUUGUAGAAAAUAAUUAUUUUGCAGUUUUCUUGUUACUACUAUUAUUAUUAAUUA ----ssRNAplot: ...((((((((((....))))))))))....(((((((((((((...............)))))))))))))............. ----hitGC: 0.176471 ----pairStats: 23,0,1,10 hit 4 : 796526 796610 (fwd) 25.37 bits :::<<<<<<<<<<_____>>>>>>>>>>----<<<<<<<<<<<<<_______________ 1 UAgaAAgaugCuCCUUGUGaGuguuUUuaaaUAaGCAUAGAGAAagUCaUUUuGcgGuGa 60 UAGA:A+ :::U C UGU A::: +U:UAA+U G:A: :A: A U AUUUUGC+GU 796526 UAGAGAUUAAAUUC-UGUUAGUGUUUUUAAUUUUGUAGAAAAUAA-UUAUUUUGCAGUU- 796582 __>>>>>>>>>>>>>:::::::..:::: 61 AuuUUCUCUAUGCuUUUAUUAU..AUCA 86 +U U :U: :U:C UUAUUAU AU A 796583 UUCUUGUUACUACUAUUAUUAUuaAUUA 796610 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #736,emb|8254664| 501920 bp 2 contigs ----isReversed: 1 ----hitSequence: UAUAUUAUUCUCCUUUUUUAUUGUUUUUUUUAAGGAAAAUUAAAAUUAUUUUGGGAAAUUUCUAUUUUUUUUUUUAUUAUUGCA ----ssRNAplot: ...(((((((((......)))))))))....(((((((((((((................)))))))))))))........... ----hitGC: 0.142857 ----pairStats: 23,1,3,7 hit 5 : 175202 175119 (rev) 26.99 bits :::<<<<<<<<<<_.____>>>>>>>>>>----<<<<<<<<<<<<<______________ 1 UAgaAAgaugCuCC.UUGUGaGuguuUUuaaaUAaGCAUAGAGAAagUCaUUUuGcgGuG 59 UA+A +AU U:C UU U:A GU+ U +UAA: A A: :A A U AUUUUG G+ 326719 UAUAU-UAUUCUCCuUUUUUAUUGUU-UUUUUUAAGGAAAAUUAAAAUUAUUUUGGGAAA 326776 ___>>>>>>>>>>>>>::::::::::: 60 aAuuUUCUCUAUGCuUUUAUUAUAUCA 86 +UU U: :U U :UUUUAUUAU CA 326777 -UUUCUAUUUUUUUUUUUAUUAUUGCA 326802 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #768,emb|8254815| 909308 bp 16 contigs ----isReversed: 0 ----hitSequence: UAUAAAUAAUCCUUUUGAAUAAACUUAAUAGUAAGCAUAAAUACUUUAAAGUAUAAUAUCAUUAUGAUUUUAGUAUAUUA ----ssRNAplot: ...((((((((.....)))))..)))......(((((((((((.............)))..))))))))........... ----hitGC: 0.15 ----pairStats: 23,4,0,3 hit 6 : 474294 474373 (fwd) 28.10 bits :::<<<<<<<<<<_.____>>>>>>>>>>-..---<<<<<<<<<<<<<____________ 1 UAgaAAgaugCuCC.UUGUGaGuguuUUua..aaUAaGCAUAGAGAAagUCaUUUuGcgG 57 UA+AA: :::UCC UU UGA:::+ :UUA A UAA CAUA: A A UUU ++G 474294 UAUAAA--UAAUCCuUU-UGAAUAAACUUAauAGUAAGCAUAA--AUA----CUUUAAAG 474344 _____>>>>>>>>>>>>>::::::::::: 58 uGaAuuUUCUCUAUGCuUUUAUUAUAUCA 86 U +A+U UC :UAUG UUUUA UAUAU A 474345 UAUAAUAUCAUUAUGAUUUUAGUAUAUUA 474373 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #876,emb|8254691| 686164 bp 4 contigs ----isReversed: 1 ----hitSequence: UGAAAAUUUAAUGUAAAUUUAUUUAUAAUAUAAUAAAGAAAACCUUUACAUUAACUAUGUUCUUUAUAUUUGAUUAUAUAA ----ssRNAplot: ...((((((((((..))))))))))....((((((((((((.................))))))))))))........... ----hitGC: 0.123457 ----pairStats: 23,1,0,7 hit 7 : 209084 209004 (rev) 27.34 bits :::<<<<<<<<<<_____.>>>>>>>>>>----<<<<<<<<<<<<<______________ 1 UAgaAAgaugCuCCUUGU.GaGuguuUUuaaaUAaGCAUAGAGAAagUCaUUUuGcgGuG 59 U+ :AA+: ::U U A:: :+UU: AAUA :AUA:AGAA: C+UU + + 477081 UGAAAAUUUAAUG----UaAAUUUAUUUAUAAUAU-AAUAAAGAAAACCUUUACAUUAAC 477135 ___>>>>>>>>>>>>>::::::::::: 60 aAuuUUCUCUAUGCuUUUAUUAUAUCA 86 +AU:UUCU:UAU: UU AUUAUAU A 477136 UAUGUUCUUUAUA-UUUGAUUAUAUAA 477161 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #1320,emb|8254377| 298147 bp 1 contigs ----isReversed: 0 ----hitSequence: UGAAAAAAUAUUUUUUUAUUUAUUUUUUUGCUUAAAAAAAUAAAAUAUUCGUUUAUCAUUAAUUUUUCUCUAUUUUUUUCUAUAUAA ----ssRNAplot: ...((((((((((......))))))))))....(((((((((((((................)))))))))))))............ ----hitGC: 0.103448 ----pairStats: 23,0,0,7 hit 8 : 250068 250154 (fwd) 25.27 bits :::<<<<<<<<<<_.____>>>>>>>>>>----<<<<<<<<<<<<<______________ 1 UAgaAAgaugCuCC.UUGUGaGuguuUUuaaaUAaGCAUAGAGAAagUCaUUUuGcgGuG 59 U+ AAA:A ::: UU U ::: U:UUU+ +UAA::A A A:AA U UUU ++U 250068 UGAAAAAAUAUUUUuUUAUUUAUUUUUUUGCUUAAAAAAAUAAAAUAUUCGUUUAUCAUU 250127 ___>>>>>>>>>>>>>::::.::::::: 60 aAuuUUCUCUAUGCuUUUAU.UAUAUCA 86 A+ UU:U U U::UUUU U UAUAU A 250128 -AAUUUUUCUCUAUUUUUUUcUAUAUAA 250154 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #1352,emb|8254529| 123311 bp 1 contigs ----isReversed: 1 ----hitSequence: UAAAAAUUUAACUUUUAUGCUUAAUUUGAUUUUUUCUAUUAAAAAAUAAAUUUCAUAAAUUAUUUUAUUGAUAGAUUAAUUCAUAUAUCA ----ssRNAplot: ...(((((((((......).)))))))).....(((((((((((((.................))))))))))))).............. ----hitGC: 0.111111 ----pairStats: 23,1,1,4 hit 9 : 115749 115660 (rev) 26.62 bits :::<<<<<<<<<<_.____>>>>>>>>>>-.---<<<<<<<<<<<<<_____________ 1 UAgaAAgaugCuCC.UUGUGaGuguuUUua.aaUAaGCAUAGAGAAagUCaUUUuGcgGu 58 UA AA+:::: C UU UG ::::+UU A +U: :AU :A:AAA + AUUU+ ++ 7563 UAAAAAUUUAA-CUuUUAUGCUUAAUUUGAuUUUUUCUAUUAAAAAAUAAAUUUCAUAAA 7621 ____>>>>>>>>>>>>>::::...::::::: 59 GaAuuUUCUCUAUGCuUUUAU...UAUAUCA 86 +AUUUU:U: AU: :U AU UAUAUCA 7622 UUAUUUUAUUGAUAGAUUAAUucaUAUAUCA 7652 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #1421,emb|8254548| 714158 bp 3 contigs ----isReversed: 1 ----hitSequence: UAAAUAGAUAAUAAUUGUUUUAACAAUCAGUAAUAAAAAAAUAAAUUUUAAAAUAAUAUUUGUUUUUUAUAUUAUUUAUACCA ----ssRNAplot: ...(((((((((.)))))))))......(((((((((((((.................)))))))))))))............ ----hitGC: 0.0963855 ----pairStats: 23,1,3,5 hit 10 : 214470 214388 (rev) 28.58 bits :::<<<<<<<<<<_____>>>>>>>>>>-..---<<<<<<<<<<<<<_____________ 1 UAgaAAgaugCuCCUUGUGaGuguuUUua..aaUAaGCAUAGAGAAagUCaUUUuGcgGu 58 UA : AGAU::U A::GUUU :A A+ :::A A:A:AAA + AUUUU +++U 499689 UAAAUAGAUAAUA------AUUGUUUUAAcaAUCAGUAAUAAAAAAAUAAAUUUUAAAAU 499742 ____>>>>>>>>>>>>>::::.::::::: 59 GaAuuUUCUCUAUGCuUUUAU.UAUAUCA 86 A++UUU:U:U U::: UUAU UAUA+CA 499743 AAUAUUUGUUUUUUAUAUUAUuUAUACCA 499771 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #1430,emb|8254552| 244997 bp 3 contigs ----isReversed: 0 ----hitSequence: UAGAAAAUUGUUUCAAUUUCUUUAGAUUUAUCGUAAAUAUAAUAAUUAUUUAUUUUACAAUUUAAUCAUUAUAUUUUUAAUAUAUUA ----ssRNAplot: ...((((((((((......)))))))))).....(((((((((((....................)))))))))))........... ----hitGC: 0.103448 ----pairStats: 23,2,2,5 hit 11 : 94287 94373 (fwd) 27.19 bits :::<<<<<<<<<<_..____>>>>>>>>>>-.---<<<<<<<<<<<<<.___________ 1 UAgaAAgaugCuCC..UUGUGaGuguuUUua.aaUAaGCAUAGAGAAa.gUCaUUUuGcg 56 UAGAAA: :G:: C UU U ::U: :UUUA UAA::AUA: :A U AUUUU C+ 94287 UAGAAAAUUGUUUCaaUU-UCUUUAGAUUUAuCGUAAAUAUAAUAAUUaUUUAUUUUACA 94345 ______>>>>>>>>>>>>>::::::::::: 57 GuGaAuuUUCUCUAUGCuUUUAUUAUAUCA 86 +U +A+ U: :UAU::UUUUA UAUAU A 94346 AUUUAA--UCAUUAUAUUUUUAAUAUAUUA 94373 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #1525,emb|8254572| 198165 bp 7 contigs ----isReversed: 0 ----hitSequence: UAAAAUUAAAUUAAACUAAUAUUUUUAAAAAUAAGUAAUUACAUCUUAUAGAUUUUUAUAAUUAUUUUUUUAUUAUAUCA ----ssRNAplot: ..(((.(((((...))))))))....(((((((((((((.................)))))))))))))........... ----hitGC: 0.075 ----pairStats: 23,2,0,6 hit 12 : 174274 174353 (fwd) 25.28 bits :::<<<<<<<<<<_____.>>>>>>>>>>----<<<<<<<<<<<<<______________ 1 UAgaAAgaugCuCCUUGU.GaGuguuUUuaaaUAaGCAUAGAGAAagUCaUUUuGcgGuG 59 UA A A+::::U U A:::: U U +UAA::AUA:::A +CAU UU +G 174274 UA-AAAUUAAAU-----UaAACUAA-UAUUUUUAAAAAUAAGUAAUUACAUCUUAUAGAU 174326 ___>>>>>>>>>>>>>::::::::::: 60 aAuuUUCUCUAUGCuUUUAUUAUAUCA 86 ++U U:::UAU::UUUUAUUAUAUCA 174327 UUUUAUAAUUAUUUUUUUAUUAUAUCA 174353 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #1668,emb|8254748| 306323 bp 5 contigs ----isReversed: 0 ----hitSequence: UAAAAAUAUGAUAGUCUUUUUAAUUUUUAUUUAAAUAAACAAAAAUAUUGAAAGAAUGUAUUUUUUUUAUUUUUUUAUCUUAUCA ----ssRNAplot: ...((((((((((....))))))))))....((((((((((((..................))))))))).)))........... ----hitGC: 0.105882 ----pairStats: 23,1,1,5 hit 13 : 139232 139316 (fwd) 30.19 bits :::<<<<<<<<<<_____>>>>>>>>>>----<<<<<<<<<<<<<___________.___ 1 UAgaAAgaugCuCCUUGUGaGuguuUUuaaaUAaGCAUAGAGAAagUCaUUUuGcg.GuG 59 UA AAA+ :G::: U U:::U: +UUU A+U:A: AUA:A AAA + AUU +G +UG 139232 UAAAAAUAUGAUAG-UCUUUUUAAUUUUUAUUUAA-AUAAACAAAAAUAUUGAAAGaAUG 139289 ___>>>>>>>>>>>>>::::::::::: 60 aAuuUUCUCUAUGCuUUUAUUAUAUCA 86 +AUUUU U:UAU :U:UUAU UAUCA 139290 UAUUUUUUUUAUUUUUUUAUCUUAUCA 139316 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #1687,emb|8254754| 392787 bp 12 contigs ----isReversed: 0 ----hitSequence: UAGAAAUGAAGUUUUAAAAUAAAUUUUAUAAAUUAAAUGAUGUAAUUUAUUUUAUGAUUAAUUGCUUCAUAAUUUUAUUAUAUCC ----ssRNAplot: ...((((((((......)))))..)))......((((((((((((................)))))))))).))........... ----hitGC: 0.129412 ----pairStats: 23,3,1,6 hit 14 : 319500 319584 (fwd) 25.84 bits :::<<<<<<<<<<_.____>>>>>>>>>>-..---<<<<<<<<<<<<<____________ 1 UAgaAAgaugCuCC.UUGUGaGuguuUUua..aaUAaGCAUAGAGAAagUCaUUUuGcgG 57 UAGAAA : : UU : :+UUUUA AAU:A :AU:: G AA U AUUUU G+ 319500 UAGAAA--UGAAGUuUUAAAAUAAAUUUUAuaAAUUA-AAUGAUGUAAUUUAUUUUAUGA 319556 _____>>>>>>>>>>>>>::::::::::: 58 uGaAuuUUCUCUAUGCuUUUAUUAUAUCA 86 U A+UU C ::AU: U:UUAUUAUAUC 319557 UU-AAUUGCUUCAUAAUUUUAUUAUAUCC 319584 ----endhit Found 15 hits. done 2.08166e+08 nucs (frac lets thru so far=0.009118762, 2d-fracLetsThru=0.00471892). Filter report: done 2.08166e+08 nucs (frac lets thru so far=0.316101281, 2d-fracLetsThru=0.200271). Filter report: done 6.58016e+07 nucs (frac lets thru so far=0.0288475958, 2d-fracLetsThru=0.0235627). FULL: done 2.08166e+08 nucs (frac lets thru so far=0.009118762, 2d-fracLetsThru=0.00471892). CPU time: 7701.80u 1.99s 02:08:23.78 Elapsed: 02:08:47 DONEdoneDONEdone